What you're seeing as "nature knowing what's best" is really just life being able to function with all kinds of random genes all over the place, because the core biochemical pathways are close enough.
We have turned seeds into the equivalent of Gillette razors. A farmer buys patented seeds and the complimentary chemical to kill everything else.
The problem is that as farming has turned into a big dumb business, centuries of best practices with respect to land management are getting tossed. Farmers near where I grow up (who are left) don’t rotate and are being ground into bankruptcy as larger and larger entities dominate.
I feel like this is putting too much faith in "natural" methodologies.
Eg, who's to say a cross breeding solution is less dangerous than a GM solution?
If the concern is that it may take 50 years to know the GM is bad, why are we assuming the non-GM is good now? You could say that people have been cross breading for many many generations, but i'm unsure why we'd know that one cross breed being safe means all crossbreeds are safe. I'm not inherently defending GM. I'm attacking the notion that man made tricks like cross breeding are inherently safe.
I think the fear around gmo is that food will be less healthy. The same way prepared food takes a few elements of food mixes with chemicals to get strong favours without the depth of flavour. They do this to save costs. GMO companies are making seeds that create plants that do not get eaten by pests. It sounds great until we realize those plants have a toxic substance inside that harms us.
Cross-breeding allows nature to combine things that fit together in all of the right places. And we just don't know how that even happens, or why. We don't understand nature's algorithm for DNA. No even the tip of the iceberg.
Sure, nature isn't always correct, but does thing properly 99.999% of the time. And that's good enough.
It is utterly incomparable to GM done by humans ~ genes are inserted, but the results are not equivalent to what is done by nature, because we don't understand DNA enough to know where we should be placing the inserted DNA, so that things don't massively fuck up inexplicably somewhere down the line.